Can I fix the error with Box12 of W-2 greater than the limit due to change of employment? I received 1099-R for the fix of over contribution and entered it already.

no leave it.  there is no error. many box 12 entries don't go anywhere  changing box 12 for the over-contribution won't change your taxable compensation.  that's what entering the 1099-R with the correct code does.